Thanks. What crossover on the L/R speakers (and confirm they're set to small) are you using? What record(s) are you using for test material? What inputs and types of connection are in use when the sub works? Is the input assignment, for the CD and DVD inputs you've tried, set for analog input?
The manual indicates stereo mode should include the sub. When you see the settings LFE or LFE+Main, can you make changes to the setting? (looking at page 84 it indicates that the setting of sub on/off, page 77, must be set to on to make this selection).
You might try a reset, too (soft reset by unplugging it for a while I'd try first, then microprocessor/system reset but you'll lose saved settings with the microprocessor/system reset).